Yes there are many items that never made production. A few years ago a major auction house sold items from Dick Kughn's collection that were from the Lionel Archives. Over 20 years ago an east coast house sold items from Lou Hertz's collection, that came from the prewar archives. Both of these auctions featured too many unique items and variations of items to list, that never made production. There is a TM or Greenberg book that features many of the items, everything from a LL Jr Hiawatha loco to a nuclear reactor model.
Marx had a similar archives auction in the 1970's or 80's that featured never-produced Marx items.
The bottom line is that yes many items come out of a companies' R&D departments, were probably shown to a committee or just to "the old man" and were rejected for reasons of cost, lack of interest or other. These items end-up on shelves in the archives gathering dust, until collector interest pries them out and they end-up in individual collections.
I could tell a similar story of prototype or R&D items from when I owned and managed the Marx Trains company from 1991 to 2004. We had hundreds of prototypes, some went to production, some just gathered dust. It is an interesting area of collecting. There are many R&D items out there, you just have to look.
